As stated by the Doctrine Configuration Reference by default logging of the SQL connection is set to the value of kernel.debug, so if you have instantiated AppKernel with debug set to true the SQL commands get stored in memory for each iteration.
You should either instantiate AppKernel to false, set logging to false in you config YML, or either set the SQLLogger manually to null before using the EntityManager
$em->getConnection()->getConfiguration()->setSQLLogger(null);